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Background This study explores the profound links between rituals and native trees in Guji society, focusing on their symbolic, cosmological, and socio-spiritual significance in the Gadaa system. Methods: Employing interviews, transect walks, and focus group discussions, data were collected from 43 purposively and snowball-sampled participants, including Gadaa leaders, elders, women, youth, and cultural experts. The analysis was conducted through thematic analysis and qualitative description. The findings The findings reveal that native trees—such as Euphorbia candelabrum var. bilocularis (Hadaammaa), Ficus vasta Forssk (Qilxaa), Vachellia horrida subsp. Benadirensis (Hurbuu), Afrocarpus gracilior (Birbissa), and Olea europaea subsp. africana (Ejersaa )—are sacred entities central to rituals like supplication and ancestral commemoration, embodying ecological and cultural harmony as eco-cultural synergy. These trees are protected through taboos and customary rules, reflecting a belief system that personifies them as divine gifts essential for the prosperity and resilience of people. However, deforestation, agricultural expansion, and cultural erosion threaten this eco-cultural synergy. Despite challenges, the Guji employ adaptive strategies, including replanting sacred trees and restorative rituals. Conclusion The culturally constructed and symbolically validated connections between rituals and trees—forming an eco-cultural synergy—serve as a testament to a society’s harmonious relationship with nature, where local belief systems and ecology coalesce into sustainable coexistence. Preserving these links underpins the conservation of trees as biocultural diversity hotspots and sustains cultural practices. Thus, there should be implementation of integrated conservation measures that address both ecological and cultural dimensions of native trees. This approach should prioritize community engagement, policy reinforcement, and sustainable practices to preserve the biocultural diversity of Guji society against the pressures of modernity.